This page collects observations, interpretations, and consequences for action about Microbiology in general of SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[Sources]], please use that page, instead of posting your content here. If you have specific microbiological topics that warrant a separate page, please create one.

=What is already known=
* Laboratory surge capacity is a critical success factor in pandemic preparedness
* ECDC has surveyed laboratory capacity in the EU (EULabCap) and reported in 2016. <Ref Name=“EULABCAP”> European Centre for Disease Prevention and Control. European Centre for Disease Prevention and Control. [https://www.ecdc.europa.eu/sites/default/files/documents/2016_EULabCap_EUreport_web_300418_final.pdf EU Laboratory Capability Monitoring System (EULabCap)] – Report on 2016 survey of EU/EEA country capabilities and capacities. Stockholm: ECDC; 2018</ref>
**
** Outbreak Assistance Laboratories in the Netherlands were found in 2009 to have sufficient capacity to process xxx samples per month of BSL3 respiratory pathogens, in addition to the routine diagnostics.<Ref name=“LvAsten”> Asten, L. van, Lubben, M. van der, Wijngaard, C. van den, Pelt, W. van, Verheij, R., Jacobi, A., Overduin, P., Meijer, A., Luijt, D., Claas, E., Hermans, M., Melchers, W., Rossen, J., Schuurman, R., Woffs, P., Boucher, C., Schirm, J., Kroes, L., Leenders, S., Galama, J., Peeters, M., Loon, A. van, Stobberingh, E., Schutten, M., Koopmans, M. Strengthening the diagnostic capacity to detect Bio Safety Level 3 organisms in unusual respiratory viral outbreaks. Journal of Clinical Virology: 2009, 45(3), 185-190</ref>

==Observation==
* Large differences exist between EU countries in numbers of Corona tests performed per capita (ref)
* Since 11 March, the Netherlands indicated that not all COVID19 suspect cases could be tested, due to limited capacity. The bottleneck are reagents, according to labs. By 7 March, 6000 tests had been performed <Ref name=“Ourworldindata”> https://ourworldindata.org/coronavirus-testing-source-data</ref>, after which no data on testing were shared.

==Analysis and interpretation==
* Existing lab capacity surveys may have looked at ‘theoretical capacity’, but clearly did not take into account dependency on supply of reagents.
* Most corona diagnostics depend on automated, high-throughput devices, which use proprietary materials. If any of those materials get out of stock, machines doe not work, even when alternative (non proprietary) materials are used.
* Manual alternatives exist, but that requires specially trained lab personnel.
==Consequences for action==
* In future, laboratory capacity surveys should not only take into account if labs are qualitatively able to perform the tests, but the quantitative capacity is important as well. This should include an analysis of dependencies, such as of external supply chains and amount of competent staff to scale up manual testing, if necessary.

=References=

Team Performance

2020-03-16T11:01:40Z

Arnold: Created page with "This page collects observations, interpretations, and consequences for action about Team Performance in COVID19 Response. Please observe the structure of the page, when you ad..."

This page collects observations, interpretations, and consequences for action about Team Performance in COVID19 Response. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[transmission routes]], please use that page, instead of posting your content here.

=What is already known=
* Team performance (both under pressure and sustained) is an important aspect of an emergency response.
* double tasking (minimum of two people who share the same task and knowledge) is imperative for response-continuity.
* Teams need to take time to look each other in the eye and focus on operational knowledge (how do we do our work, in response to Covid-19) and also how do we continue to work as an effective team over a prolonged period of time.

=Team health=
==Observations==
* Team members of response teams (health care, public health, community response) get sick too.

==Analysis and interpretation==
* Response teams with a critical role in the containment, mitigation or management of the COVID19 crisis become less effective or drop out completely if business continuity is not ensured.

==Consequences for action==
* think ahead as team members will become ill and be replaced by other staff.
* Make sure that teams keep an effective and up-to-date log, so that others can find their way in once they become new team members.

=References=

Case Definition issues

2020-03-16T10:54:01Z

Arnold:

This page collects observations, interpretations, and consequences for action about the case definition of SARS-CoV2 in general. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[transmission routes]], please use that page, instead of posting your content here.

=What is already known=
==2 March 2020==
WHO Case Definition:
* Suspect case:
** anyone with COVID symptoms + no other etiology + positive travel in a country with local transmission
OR
** Anyone with COVID symptoms + close contact to a confirmed case
OR
** a hospitalized SARI case + no other etiology

ECDC Case Definition:

=Implementing case definition changes=
==Observations==
* WHO (and ECDC) published their new recommendation on COVID case definition on March 2: this contained a significant shift from the previous approach
** Countries were not informed in advance by WHO/ECDC that this was coming out. Some had just updated the national protocol and distribute it widely to hospitals and PH authorities, moments before receiving the updated approach from WHO.
** This created much anxiety. Experts were surprised that WHO did not distinguish between countries with "local transmission". De facto, the majority of returning travelers now came from Corona-Risk areas.
** This new approach had a significant impact on testing demand, generating discussions on how to deal with that. In addition, it impacted on case identification among the hospitalized SARI cases. Much time was spent (and lost?) on discussing priorities for testing.

==Analysis and interpretation==
* This led to some countries still having no updated policy two weeks after the new case definitions were published, and as a consequence, most of the medical staff was still focussing on people coming from the original high-risk areas or contact with a confirmed case only; as a consequence, new COVID19 cases remain unreported.
* Some experts strongly disagree with WHO about the need to exclude other etiology first. The recommendation is probably aimed to decrease the need for COVID-19 testing, but the fact that this leads to a significant delay in the COVID-19 diagnosis (and thus increased exposure of healthcare workers to undetected COVID-19) some public health experts find hard to digest.

==Consequences for action==
* Countries should be prepared to rapidly shift gear when international case guidelines change. During pandemics, it is unrealistic to expect that coordinating organizations such as WHO and ECDC can predict when they will change guidelines, so one cannot expect timetables for this.
** Communication channels from national public health bodies to health care professionals should allow for such rapid changes, and a platform of rapid exchange of information and advice would be beneficial.
** Health care providers on their term should be prepared to receive rapidly changing guidelines during international infectious disease crises. What is considered a constant among all large pandemics, is that gaps in knowledge are rapidly filled; therefore new insights have to be translated to an improvement of prevention and control in a timely and efficient way.
** The best way for countries to prepare for this, is to have regular simulation exercises that take these issues into account.

=Topic 2=
==Observations==

==Analysis and interpretation==

==Consequences for action==

=References=

Early Warning and Surveillance

2020-03-16T10:52:41Z

Arnold:

This page collects observations, interpretations, and consequences for action about Early Warning of SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[Sources]], please use that page, instead of posting your content here.

=What is already known=

=Topic 1=
==Observations==
==Analysis and interpretation==
==Consequences for action==

=References=

Pandemic Preparedness

2020-03-16T10:52:13Z

Arnold:

This page collects observations, interpretations, and consequences for action about Preparedness for SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[Sources]], please use that page, instead of posting your content here.

=What is already known=

=Topic 1=
==Observations==
==Analysis and interpretation==
==Consequences for action==

=References=

Microbiology

2020-03-16T10:51:38Z

Arnold:

Contagiousness

2020-03-16T10:50:46Z

Arnold:

This page collects observations, interpretations, and consequences for action about Contagiousness of SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[Sources]], please use that page, instead of posting your content here.

=What is already known=

=Topic 1=
==Observations==
==Analysis and interpretation==
==Consequences for action==

=References=

Risk factors for severe disease

2020-03-16T10:50:11Z

Arnold:

This page collects observations, interpretations, and consequences for action about Risk Factors of SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about [[Sources]], please use that page, instead of posting your content here.

=What is already known=

=Topic 1=
==Observations==
==Analysis and interpretation==
==Consequences for action==

=References=

2020-03-16T10:40:18Z

Arnold: